Procedures for qualitatively or quantitatively determining the presence of particular organisms or viruses in a test sample routinely rely upon nucleic acid-based probe testing. To increase the sensitivity of these procedures, an amplification step is often included to increase the copy number of potential nucleic acid target sequences present in the test sample. During amplification, polynucleotide chains containing the target sequence and/or its complement are synthesized in a template-dependent manner from ribonucleoside or deoxynucleoside triphosphates using nucleotidyltransferases known as polymerases. There are many amplification procedures in general use today, including the polymerase chain reaction (PCR), Q-beta replicase, self-sustained sequence replication (3SR), transcription-mediated amplification (TMA), nucleic acid sequence-based amplification (NASBA), ligase chain reaction (LCR), strand displacement amplification (SDA) and loop-mediated isothermal amplification (LAMP), each of which is well known in the art. See, e.g., Mullis, “Process for Amplifying Nucleic Acid Sequences,” U.S. Pat. No. 4,683,202; Erlich et al., “Kits for Amplifying and Detecting Nucleic Acid Sequences,” U.S. Pat. No. 6,197,563; Walker et al., Nucleic Acids Res., 20:1691-1696 (1992); Fahy et al., “Self-sustained Sequence Replication (3SR): An Isothermal Transcription-Based Amplification System Alternative to PCR,” PCR Methods and Applications, 1:25-33 (1991); Kacian et al., “Nucleic Acid Sequence Amplification Methods,” U.S. Pat. No. 5,399,491; Davey et al., “Nucleic Acid Amplification Process,” U.S. Pat. No. 5,554,517; Birkenmeyer et al., “Amplification of Target Nucleic Acids Using Gap Filling Ligase Chain Reaction,” U.S. Pat. No. 5,427,930; Marshall et al., “Amplification of RNA Sequences Using the Ligase Chain Reaction,” U.S. Pat. No. 5,686,272; Walker, “Strand Displacement Amplification,” U.S. Pat. No. 5,712,124; Notomi et al., “Process for Synthesizing Nucleic Acid,” U.S. Pat. No. 6,410,278; Dattagupta et al., “Isothermal Strand Displacement Amplification,” U.S. Pat. No. 6,214,587; and Lee et al., Nucleic Acid Amplification Technologies: Application To Disease Diagnosis (1997).
Nucleic acid products formed during an amplification procedure (i.e., amplicon) can be analyzed either during the course of the amplification reaction (real-time) or once the amplification reaction has been generally completed (end-point) using detectable probes. While the probes are designed to screen for target-containing amplicon, other products may be produced during an amplification procedure (e.g., primer-dimers formed in a typical PCR reaction) that have the potential to interfere with the desired amplification reaction. Following completion of the amplification procedure and exposure to detectable probes, the resulting reaction mixture is discarded.
During the steps of an assay or synthesis procedure which includes an amplification procedure, it is possible to contaminate work surfaces or laboratory equipment with nucleic acids used or formed in the assay through spills, mishandling, aerosol formation, etc. This nucleic acid can then carry-over and contaminate future amplification and other nucleic acid assay procedures performed using the same laboratory equipment and/or on the same work surfaces. The presence of carryover products can result in the unwanted consumption of amplification reagents or, in the case of target-containing amplicon from a previous amplification procedure, it can lead to an erroneous result, as amplification procedures are capable of detecting the presence of even minute amounts of target nucleic acid. In the case of a synthetic amplification reaction, the desired nucleic acid product may become contaminated by carry-over products and/or synthesis yields may be reduced.
Various methods have been devised to limit carryover contamination. A PCR amplification product, for example, can be deactivated from further amplification by irradiation with UV light. See Ou et al., BioTechniques, 10:442-446 (1991); and Cimino et al., Nucleic Acids Res., 19:99-107 (1991). Such irradiation in the absence or presence of a DNA binding photoactivatable ligand (e.g., isopsoralen) makes the product DNA nonamplifiable but retains the specific hybridization property. In addition, use of a 3′-ribose primer in a PCR reaction produces nucleic acid that can be readily destroyed by an alkali (e.g., NaOH). See Walder et al., Nucleic Acids Res., 21:4339-4343 (1993). Similarly, other procedures are used to produce specific modified nucleic acids that can be selectively destroyed by treatment with a specific enzyme. Such modified nucleic acids have been produced by amplification in the presence of dUTP as a substrate in a PCR reaction. Deoxy U-containing product DNA can be deactivated by a U-specific enzyme making the DNA nonamplifiable. See Integrated DNA Technologies Technical Bulletin, Triple C primers (1992); and Longo et al., Gene, 93:125-128 (1990). Many of these methods function well with DNA but require expensive reagents and affect the course of the amplification procedure (e.g., requiring longer times and specific reagents).
In a preferred method, work surfaces and laboratory equipment exposed to nucleic acid products are treated with a 50% bleach solution (i.e., a bleach solution containing about 2.5% to about 3.25% (w/v) sodium hypochlorite) to deactivate nucleic acids. See GEN-PROBE® APTIMA COMBO 2® Assay Package Insert, IN0037 Rev. A/2003-08. While this bleach solution is effective at deactivating nucleic acids present on treated surfaces, it tends to create noxious fumes in poorly ventilated areas and corrodes laboratory equipment over time. Therefore, it is an object of the present invention to provide a formulation containing a nucleic acid deactivating agent that is stable in solution, has a tolerable odor, and which is non-corrosive or is substantially less corrosive than a standard 50% bleach solution.